Agriculture in Indiahas been heavily dependent on the use of inorganic fertilizers and pesticides for the past 4 to 5 decades. Such practices has had negative environmental consequences in terms of reduced ability of the agro-ecosystems in regulating (maintenance of hydrological services, water quality, carbon sequestration) and supporting (soil microbial diversity, soil structure and fertility, nutrient cycling, biological pest control, pollination) Ecosystem Services (ES). Bioeconomy in agriculture, which stresses on supply of food and agricultural outputs through extraction and use of high quality inputs from renewable resources, gains significance in this context. Use of renewable factors of production reduces agriculture-induced environmental impacts, reduces the yield gaps and strengthens agro-ecosystems ability to regulate and support ES. Organic farming approach that promotes bioeconomy in agriculture is highly dependent on diverse soil microflora consisting of beneficial microbes. They facilitate ecological services such as nutrient cycling, disease control, drought tolerance, degradation of organic matter, water lifting etc. Biofertilizers and bio-pesticides are the biological products necessary to augment the soil microflora, in this way they are linked to building bioeconomy in agriculture. The renewable use of bio resources called bio-inputs henceforth primarily offers a mean to reduce the dependence on chemical inputs and sustain the provision of valuable ES. These bio-inputs play an integral role in maintaining soil quality nutrient fixation, mobilization and solubilisation processes, induces abiotic and biotic stress tolerance and manages pest and diseases through maintaining a healthy prey-predator balance in environment. Microbial based bio products are an important input for organic and sustainable agriculture production systems as it works on the same principles as bio-economy and could be considered as an important pathway for promoting bio-economy in agriculture. The recent progress in research and development of microbial consortium and microbiome approaches adds value to the use of bio-inputs in agriculture. This paper is an attempt to detail the processes through which the principles of bioeconomy in the soil ecosystem could be effectively harnessed to achieve productivity in perpetuity by the use of renewable microbial bio resources.